3. depends on the magnitude of the score, but tipically the lowest few
scores do not represent meaningfully different models.
reason for 1 and 2 is that modeller scores solely depend on the
violation of restrainst, adding or removing some of them will setup a
new relative pseudo-energy scale.
Dan Thomas Major wrote:
> I have a few question concerning the energy terms computed by
> 1) Can the energy of a model computed with loop-modeling be compared
> to the energy of a model computed without?
> 2) Can the energy of a model with an additional constraint added (like
> a specific distance constraint) be compared to the energy of a model
> without that specific constraint?
> 3) What kind of energy difference can be considered to reflect a
> significant difference in the quality of models?
> Dan Thomas Major
> Dan Thomas Major (at Dr. B. Fischer's lab)
> Bar-Ilan University
> Phone: 972-3-5317785
> Fax: 972-3-5348730
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras